Converting a mesh to voxels
As Chebhou suggested in the comments, the 2D image stack can be achieved with dynamic painting an animated plane.


Add a plane, and animate it to pass through the main mesh
In the physics panel of the main mesh, enable Dynamic Paint and make it a brush
In the physics panel of the plane, enable Dynamic Paint and make it a canvas with these settings:


Format: Image Sequence
Dry time: 1
Dissolve time: 1

In the Dynamic Paint Output panel, click "Bake Image Sequence" to write out the plane/mesh intersection at each frame of the animation.